A solution of 5X TBE buffer was prepared to use for gel preparation in a 50ml Falcon tube.

Gel loading buffer was taken from the lab in an Eppendorf tube.

Gel Running Buffer was prepared - 200ml 5X TBE buffer.

The pH of the buffer was checked using pH meter and found out to be equal to 8.46

The buffer was stored in a conical flask

5th October, 2013

Reagent preparation:

20% PAGE components:
6.6ml of 29:1 acrylamide
0.07ml of APS
2ml of 5X TBE Buffer
2.3μl of TEMED
Appropriate amount of water was added to make the final volume upto 10ml.

5X Running Buffer was diluted using can water

A PAGE(20% acrylamide) was run by loading the following samples in different lanes - I1L1 annealed, I1 (S2 stock), L1 (S2 stock), BI2L2 annealed, BL2 annealed, L2I2 annealed. This was done in order to detect formation of the structures I1L1 and BI2L2.

Gel 1 - Lanes are 1 : B2(2uL), 2 : B2(4uL), 3 : B2(8uL), 4 : B2(16uL), 5 : I1, 6 : L1, 7 : I1L1 annealed The lane for I1L1 shows a band higher than I1 and L1 lanes. However, both bands for I1 and L1 can not be at the same level.

This time at least the last 3 lanes showed bands that were distinctly visible !!
The first few lanes were unclear after staining with 50ml of 1X TBE + 10μL EtBr solution. Hence, the gel was stained with 1μL EtBr solution again. This caused the whole gel to become blue. Hence, more gels need to be run.

20th October, 2013

Reagent preparation:

15% PAGE components:
5ml of 29:1 acrylamide
0.07ml of APS
2ml of 5X TBE Buffer
10μl of TEMED
Appropriate amount of water was added to make the final volume up to 10ml.

A gel was run to confirm formation of our final structure and to check the correctness of strand design (it must not result in non-specific binding of I1, I2 to B). The percentage was decided to be 15 as in the previous gel, the bands stayed very near the top.